[ITK] [ITK-dev] HDF5 TransformIO broken with System HDF5

[Bradley Lowekamp]

Matt,

SimpleITK's super build passes CMAKE variable with the prefix "ITK_" to the ITK external project so customizing the ITK in the superbuild is easy. Here is the build script for the system build for the dashboard:

http://open.cdash.org/viewNotes.php?buildid=3322976

Brad

On May 9, 2014, at 12:33 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Yes [1], but it looks like ITK was not configured correctly?  I will
> try turning on the Review module...
> 
> [1] http://open.cdash.org/buildSummary.php?buildid=3320996
> 
> On Thu, May 8, 2014 at 9:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Great,
>> 
>> Hopefully it's finished by now :)
>> 
>> Brad
>> 
>> On May 7, 2014, at 5:46 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>> 
>>> Thanks, Brad.
>>> 
>>> Debug build with those packages on Ubuntu 12.04:
>>> 
>>> http://open.cdash.org/buildSummary.php?buildid=3320987
>>> 
>>> Starting SimpleITK Debug build...
>>> 
>>> On Wed, May 7, 2014 at 1:39 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> Matt on Ubuntu 12 I have the following installed:
>>>> 
>>>> libhdf5-serial-1.8.4                            install
>>>> libhdf5-serial-dev                              install
>>>> 
>>>> And on RHEL I have:
>>>> 
>>>> hdf5-devel-1.8.5.patch1-7.el6.x86_64
>>>> hdf5-1.8.5.patch1-7.el6.x86_64
>>>> 
>>>> Brad
>>>> 
>>>> On May 7, 2014, at 1:31 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>>> 
>>>>> Hi Brad,
>>>>> 
>>>>> On Ubuntu 12.04, there appears to be a number of HDF5 "-dev" packages:
>>>>> 
>>>>> libhdf5-lam-dev
>>>>> libhdf5-mpi-dev
>>>>> libhdf5-mpich-dev
>>>>> libhdf5-openmpi-dev
>>>>> libhdf5-serial-dev
>>>>> 
>>>>> Which one are you using?
>>>>> 
>>>>> Thanks,
>>>>> Matt
>>>>> 
>>>>> On Wed, May 7, 2014 at 1:23 PM, Matt McCormick
>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>> Hi Brad,
>>>>>> 
>>>>>> It looks like our code coverage for the HDF TransformIO is pretty good
>>>>>> [1], but I do not see a dashboard submission for those platforms that
>>>>>> use a system HDF5.  I will set one up on faraway.kitware and try to
>>>>>> reproduce the SimpleITK test failure.
>>>>>> 
>>>>>> Thanks,
>>>>>> Matt
>>>>>> 
>>>>>> [1] http://lorensen.github.io/VTKCodeCoverage/ITK/IO/TransformHDF5/src/index.html
>>>>>> 
>>>>>> On Wed, May 7, 2014 at 8:59 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>>>>> Hello,
>>>>>>> 
>>>>>>> I wrote some SimpleITK tests to write out HDF5 transforms. They are failing when using ITK built with system HDF5. Specifically with RHEL5 and Ubuntu 12.04. I believe this is a critical issue as it's how ITK is being built for Linux distributions.
>>>>>>> 
>>>>>>> Looking through my ITK nightly build testing directory I didn't see any hdf5 files which leads me to believe this IO transform format may not be well tested.
>>>>>>> 
>>>>>>> I would greatly appreciate some assistance on this issue.
>>>>>>> 
>>>>>>> Here is my related SimpleITK issue.
>>>>>>> https://issues.itk.org/jira/browse/SIMPLEITK-535
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Brad
>>>>>>> 
>>>> 
>> 

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